Description Usage Arguments Details Value Author(s) References Examples
View source: R/computeChIPProfile.R
computeChIPProfile
compute ChIP-seq like profile from occupancy data.
Occupancy data is computed using computeOccupancy
.
1 2 3 | computeChIPProfile(genomicProfiles, loci, parameterOptions = NULL,
norm = TRUE, method = c("moving_kernel","truncated_kernel","exact"),
peakSignificantThreshold= NULL,cores=1, verbose = TRUE)
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genomicProfiles |
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loci |
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parameterOptions |
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norm |
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method |
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peakSignificantThreshold |
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cores |
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verbose |
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computeChIPProfile
converts Transcription Factor occuapncy to a profile
resembling the one of a ChIP-seq profile. Internally a few paramters are required
to build a ChIP like profile. These parameters are either defined and stored in
a ChIPScore
object (Paramters are updated based on
your ChIP data ), a genomicProfiles
(user defined at the
start of the analysis) or a parameterOptions
(if you want to
update values as you go along)
Returns a genomicProfiles
objec containing all ChIP-seq like
profile for every combination of lambdaPWM
and boundMolecules
provided by the user.
Patrick C.N. Martin <pm16057@essex.ac.uk>
Zabet NR, Adryan B (2015) Estimating binding properties of transcription factors from genome-wide binding profiles. Nucleic Acids Res., 43, 84<e2><80><93>94.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 | #Extracting Data
data(ChIPanalyserData)
# path to Position Frequency Matrix
PFM <- file.path(system.file("extdata",package="ChIPanalyser"),"BCDSlx.pfm")
#As an example of genome, this example will run on the Drosophila genome
if(!require("BSgenome.Dmelanogaster.UCSC.dm3", character.only = TRUE)){
if (!requireNamespace("BiocManager", quietly=TRUE))
install.packages("BiocManager")
BiocManager::install("BSgenome.Dmelanogaster.UCSC.dm3")
}
library(BSgenome.Dmelanogaster.UCSC.dm3)
DNASequenceSet <- getSeq(BSgenome.Dmelanogaster.UCSC.dm3)
# Building genomicProfiles object
GPP <- genomicProfiles(PFM=PFM, PFMFormat="raw",BPFrequency=DNASequenceSet)
# Computing Genome Wide
GenomeWide <- computeGenomeWideScores(genomicProfiles = GPP,
DNASequenceSet = DNASequenceSet)
#Compute PWM Scores
PWMScores <- computePWMScore(genomicProfiles = GenomeWide,
DNASequenceSet = DNASequenceSet, loci = eveLocus, chromatinState = Access)
#Compute Occupnacy
Occupancy <- computeOccupancy(genomicProfiles = PWMScores)
#Compute ChIP profiles
chipProfile <- computeChIPProfile(genomicProfiles=Occupancy,loci=eveLocus)
chipProfile
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